NM_001194998.2(CEP152):c.2034T>G (p.Tyr678Ter) AND Microcephaly 9, primary, autosomal recessive

Germline classification:: Pathogenic/Likely pathogenic (5 submissions)
Last evaluated:: May 11, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000145609.20

Allele description [Variation Report for NM_001194998.2(CEP152):c.2034T>G (p.Tyr678Ter)]

NM_001194998.2(CEP152):c.2034T>G (p.Tyr678Ter)

Gene:

CEP152:centrosomal protein 152 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q21.1

Genomic location:

Preferred name:

NM_001194998.2(CEP152):c.2034T>G (p.Tyr678Ter)

HGVS:

NC_000015.10:g.48767448A>C
NG_027518.2:g.48699T>G
NM_001194998.2:c.2034T>GMANE SELECT
NM_014985.4:c.2034T>G
NP_001181927.1:p.Tyr678Ter
NP_055800.2:p.Tyr678Ter
NC_000015.9:g.49059645A>C
NG_027518.1:g.48699T>G
NM_001194998.1:c.2034T>G
NM_001194998.2:c.2034T>G
NM_014985.3:c.2034T>G

Protein change:

Y678*; TYR678TER

Links:

OMIM: 613529.0004; dbSNP: rs182018947

NCBI 1000 Genomes Browser:

rs182018947

Molecular consequence:

NM_001194998.2:c.2034T>G - nonsense - [Sequence Ontology: SO:0001587]
NM_014985.4:c.2034T>G - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Microcephaly 9, primary, autosomal recessive
Identifiers:: MONDO: MONDO:0013923; MedGen: C3553886; Orphanet: 2512; OMIM: 614852

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000192706	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 28, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000236533	Courtagen Diagnostics Laboratory, Courtagen Life Sciences	criteria provided, single submitter (Courtagen Life Sciences Classifications)	Pathogenic (Jan 28, 2014)	germline	clinical testing	Citation Link,
SCV000784549	Genomic Research Center, Shahid Beheshti University of Medical Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 11, 2024)	inherited	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002012250	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 2, 2021)	maternal	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004806962	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 26, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	maternal	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	inherited	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000192706.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Courtagen Diagnostics Laboratory, Courtagen Life Sciences, SCV000236533.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000784549.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From 3billion, SCV002012250.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant (PVS1_VS). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000295, PM2). The variant was observed in trans with a pathogenic variant (NM_001194998.1:c.314G>A) as compound heterozygous (3billion dataset, PM3).The variant has been reported as pathogenic (ClinVar ID: VCV000158240.10). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004806962.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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